inflexa

Molecular structure analysis, SAR triage, compound library characterization, QSAR modeling, ADMET prediction, chemical space visualization, target engagement assessment, drug perturbation connectivity scoring, and selectivity profiling

Chromatin regulation analysis — ATAC-seq, ChIP-seq, CUT&Tag/CUT&Run, differential binding, motif analysis, and scATAC-seq

Systematic drug repurposing via signature matching, target-based analysis, network proximity, genetic evidence scoring, and clinical evidence mining

Functional enrichment and pathway analysis including GSEA, ORA, ssGSEA, GSVA, and decoupler-based activity inference

Genomic variant analysis — germline/somatic SNV, structural variants, CNV, GWAS, annotation, and filtering

Metabolomics and lipidomics analysis — untargeted/targeted workflows, normalization, annotation, and pathway mapping

Multi-omics integration methods including factor analysis, supervised classification, network fusion, and causal modeling across modalities

Bulk RNA-seq and microarray differential expression analysis including method selection, batch correction, and complex experimental designs

DNA methylation analysis — array (450K/EPIC), bisulfite-seq, DMP/DMR detection, clocks, deconvolution, and EWAS

Microbiome analysis — compositional data handling, 16S/ITS amplicon, shotgun metagenomics, diversity, differential abundance, and functional profiling

Network and regulatory analysis including co-expression networks, GRN inference, PPI analysis, and TF activity scoring

Cross-cutting principles for all omics analysis — AnnData/MuData universal containers, Python-first policy, data format detection, analysis phases, and shared analytical methods

Single-cell analysis pipeline covering scRNA-seq, snRNA-seq, and CyTOF (mass cytometry) — QC, normalization, integration, clustering, annotation, differential expression, trajectory, cell communication, and TF activity inference

Spatial transcriptomics and spatial proteomics analysis covering technology-specific workflows, spatial statistics, deconvolution, and niche analysis

Jinja2 + Tailwind v4 CDN + ECharts light-themed report templating following the Inflexa Design Blueprint

Immune cell deconvolution, immune signature scoring, checkpoint expression panels, TCR/BCR repertoire analysis, tumor microenvironment characterization, and IO response prediction

Multi-modal single-cell analysis for CITE-seq, Multiome, TEA-seq, and DOGMA-seq including joint embedding, per-modality QC, and cross-modal integration

Pharmacokinetic/pharmacodynamic modeling, exposure-response analysis, clinical response classification (RECIST/iRECIST), dose-response curves, population PK covariate modeling, PD biomarker tracking, PK-PD hysteresis, and time-to-event endpoints

Proteomics analysis covering DDA, DIA, TMT/iTRAQ, Olink, and SomaScan platforms including preprocessing, normalization, differential expression, and PTM analysis

Safety pharmacology assessment, CTCAE grading, organ-specific toxicity biomarkers, CYP liability analysis, structural alerts, and drug-drug interaction evaluation

Verify harness changes at the package boundary — build dist, link the package into a scratch consumer, drive runAgent/tools/gateways against a real Postgres via podman. Use after changing @inflexa-ai/harness when the CLI does not yet consume the change.

Statistical modeling and machine learning for biomarker discovery, survival analysis, classification, regression, and model interpretation

Write database queries and mutations for the SQLite storage layer. Use when adding, modifying, or reviewing db functions in src/db/, or when the user asks how to read/write to the database.